--- layout: default title: Xons/ChIPseq.Demo ---

Sample Info

ChIPseq

single end

50 bp reads

mouse

QA/QC

Alignment

Percentage

Reads distribution

Reads distribution across the whole genome. Reads of input should distribute evenly, and reads of IP samples should be enriched at a small portion of genome regions. Bin size is 50000 bp.

Peak calling

Macs2 Peak

Macs2 peaks

Peak annotation

Genome: mm10 Ens80

Annotated peaks

Peaks with pvalue<1e-5 and reads>20 are kept.

Peak are annotated by their nearest gene features or nearest TSS.

Annotated peaks by gene feature

Annotated peaks by TSS

Peak position to gene features

Overlap_tss means peak within 1 kb of TSS.

Peak distribution to TSS

Histone modifications around peaks

Centered at TF peak center and plot the coverage of histone markers around the peaks.

GO terms of peak nearest genes

R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] plotrix_3.6-3 edgeR_3.14.0
[3] limma_3.28.21 lattice_0.20-34
[5] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4
[7] GenomicAlignments_1.8.4 Rsamtools_1.24.0
[9] Biostrings_2.40.2 XVector_0.12.1
[11] SummarizedExperiment_1.2.3 Biobase_2.32.0
[13] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[15] IRanges_2.6.1 S4Vectors_0.10.3
[17] BiocGenerics_0.18.0 knitr_1.14
[19] pander_0.6.0 scales_0.4.1
[21] pheatmap_1.0.8 RColorBrewer_1.1-2
[23] reshape2_1.4.2 ggplot2_2.2.0
[25] rmarkdown_1.1

loaded via a namespace (and not attached): [1] Rcpp_0.12.8 formatR_1.4 plyr_1.8.4
[4] bitops_1.0-6 tools_3.3.1 zlibbioc_1.18.0
[7] biomaRt_2.28.0 digest_0.6.11 RSQLite_1.0.0
[10] evaluate_0.10 tibble_1.2 gtable_0.2.0
[13] DBI_0.5-1 yaml_2.1.13 rtracklayer_1.32.2 [16] stringr_1.1.0 grid_3.3.1 XML_3.98-1.4
[19] BiocParallel_1.6.6 magrittr_1.5 htmltools_0.3.5
[22] assertthat_0.1 colorspace_1.2-7 labeling_0.3
[25] stringi_1.1.2 RCurl_1.96-0 lazyeval_0.2.0
[28] munsell_0.4.3